Genomic, transcriptomic, and metabolomic analyses provide insights into the evolution and development of a medicinal plant Saposhnikovia divaricata (Apiaceae)

Abstract

Saposhnikovia divaricata, 2n = 2x = 16, as a perennial species, is widely distributed in China, Mongolia, Russia, etc. It is a traditional Chinese herb used to treat tetanus, rubella pruritus, rheumatic arthralgia, and other diseases. Here, we assembled a 2.07 Gb and N50 scaffold length of 227.67 Mb high-quality chromosome-level genome of S. divaricata based on the PacBio Sequel II sequencing platform. The total number of genes identified was 42 948, and 42 456 of them were functionally annotated. A total of 85.07% of the genome was composed of repeat sequences, comprised mainly of long terminal repeats (LTRs) which represented 73.7% of the genome sequence. The genome size may have been affected by a recent whole-genome duplication event. Transcriptional and metabolic analyses revealed bolting and non-bolting S. divaricata differed in flavonoids, plant hormones, and some pharmacologically active components. The analysis of its genome, transcriptome, and metabolome helped to provide insights into the evolution of bolting and non-bolting phenotypes in wild and cultivated S. divaricata and lays the basis for genetic improvement of the species.

Acknowledgements

This research was supported by a Chinese Key Research and Development Project grant (2019YFC1710700) awarded to L.-M.Y., Promotion Demonstration Project of Forestry Science and Technology of China (JLT2024-30) awarded to Z.-M.H., Jilin Agricultural University high level researcher grant (JLAUHLRG20102006) awarded to J.Z.

Author contributions

Z.-M.H., A.-S.X., and J.Z. conceived the project. Z.-M.H., Y.C., and X.-Y.L. designed the experiments. Z.-H.W., Y.C., X.L., Y.-H.W., Z.-L.L, L.-M. Y., and H.L. performed most of the experiments. Z.-H.W., Y.C., X.L., Y.-H.W., L.C., B.L., Z.-M.H., and J.Z. analysed and discussed the data. Z.-H.W., A.-S.X., M.K.D., and J.Z. wrote the manuscript with comments from all authors.

Data availability

Raw sequencing reads have been deposited in the National Center for Biotechnology Information under BioProject accession number PRJNA1041486 and National Genomics Data Center under the project number PRJCA022150.

Conflict of interest statement

The authors report no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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